NeurIPS 2025

One Prompt Fits All: Universal Graph Adaptation for Pretrained Models

Yongqi Huang, Jitao Zhao, Dongxiao He, Xiaobao Wang, Yawen Li, Yuxiao Huang, Di Jin, Zhiyong Feng

Main figure for One Prompt Fits All: Universal Graph Adaptation for Pretrained Models

Abstract

Graph Prompt Learning (GPL) has emerged as a promising paradigm that bridges graph pretraining models and downstream scenarios, mitigating label dependency and the misalignment between upstream pretraining and downstream tasks. Although existing GPL studies explore various prompt strategies, their effectiveness and underlying principles remain unclear. We identify two critical limitations: (1) Lack of consensus on underlying mechanisms: Despite current GPLs have advanced the field, there is no consensus on how prompts interact with pretrained models, as different strategies intervene at varying spaces within the model, i.e., input-level, layer-wise, and representation-level prompts. (2) Limited scenario adaptability: Most methods fail to generalize across diverse downstream scenarios, especially under data distribution shifts (e.g., homophilic-to-heterophilic graphs). To address these issues, we theoretically analyze existing GPL approaches and reveal that representation-level prompts essentially function as fine-tuning a simple downstream classifier, proposing that graph prompt learning should focus on unleashing the capability of pretrained models, and the classifier should adapt to downstream scenarios. Based on our findings, we propose UniPrompt, a novel GPL method that adapts any pretrained models, unleashing the capability of pretrained models while preserving the input graph. Extensive experiments demonstrate that our method can effectively integrate with various pretrained models and achieve strong performance across in-domain and cross-domain scenarios.

Proposed method: UniPrompt

Benchmark Results

Tested on 7 datasets 5 baseline values reported too low

Tables show presented results in global context (best 3 papers + GCN + MLP).

Classic

#ModelAccuracy ↑Paper
1
GraphSAGE+CNA
0.9418 ±0.0033
2
GCN+CNA
0.9366 ±0.0048
3
TransformerConv
0.9350 ±0.0058
21
GCN
0.9004
724
MLP
0.7768
884
GPF
actual #884 vs paper #898 14 places worse
0.5760 ±0.1388
best reported
actual #884 vs paper #898 14 places worse
paper 0.5168 ±0.0952

Difference within reported uncertainty; not counted as underperformance.

paper 0.5168 ±0.0952 Δ at pub 0.0592
892
GraphPrompt
actual #892 vs paper #898 6 places worse
0.5425 ±0.0938
best reported
actual #892 vs paper #898 6 places worse
paper 0.5145 ±0.0963

Difference within reported uncertainty; not counted as underperformance.

paper 0.5145 ±0.0963 Δ at pub 0.0280
898
All-In-One
actual #898 vs paper #910 12 places worse
0.5239 ±0.1017
best reported
actual #898 vs paper #910 12 places worse
paper 0.3453 ±0.0586
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)
paper 0.3453 ±0.0586 Δ at pub 0.1786
900
Fine-tune
0.5022 ±0.0928
This paper
901
Linear-probe
0.5013 ±0.1206
This paper
902
UniPrompt
0.4995 ±0.1048
This paper
906
EdgePrompt+
0.4532 ±0.0903
This paper
909
GPPT
actual #909 vs paper #909
0.4315 ±0.0944
best reported
actual #909 vs paper #909
paper 0.4219 ±0.0642
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)

Difference within reported uncertainty; not counted as underperformance.

paper 0.4219 ±0.0642 Δ at pub 0.0096
#ModelAccuracy ↑Paper
1
CNA
0.9575 ±0.0058
2
IS-GIB
0.9390 ±0.0187
3
EERM
0.9112 ±0.0145
44
GCN
0.8033 ±0.0088
350
MLP
0.7289 ±0.0010
603
GPPT
actual #603 vs paper #887 284 places worse
0.7031 ±0.0039
best reported
actual #603 vs paper #887 284 places worse
paper 0.3742 ±0.0910
866
EdgePrompt+
actual #866 vs paper #887 21 places worse
0.4971 ±0.0225
best reported
actual #866 vs paper #887 21 places worse
paper 0.3854 ±0.0637
paper 0.3854 ±0.0637 Δ today 0.1117
868
UniPrompt
0.4929 ±0.1120
This paper
869
GPF
actual #869 vs paper #879 10 places worse
0.4489 ±0.0661
actual #869 vs paper #879 10 places worse
paper 0.4489 ±0.0661

Improvement within reported uncertainty; not highlighted.

paper 0.4489 ±0.0661 Δ at pub 0.0161
870
Linear-probe
0.4808 ±0.0696
This paper
871
GraphPrompt
actual #871 vs paper #883 12 places worse
0.4707 ±0.0309
best reported
actual #871 vs paper #883 12 places worse
paper 0.4398 ±0.0761

Difference within reported uncertainty; not counted as underperformance.

paper 0.4398 ±0.0761 Δ at pub 0.0136 Δ today 0.0309
874
Fine-tune
0.4616 ±0.0630
This paper
882
All-In-One
actual #882 vs paper #891 9 places worse
0.4436 ±0.0252
best reported
actual #882 vs paper #891 9 places worse
paper 0.3172 ±0.0278
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)
paper 0.3172 ±0.0278 Δ at pub 0.0869 Δ today 0.1264

Heterophilic Graphs

#ModelAccuracy ↑Paper
1
P^2GNN
0.9672 ±0.0147
2
DoG
0.9660 ±0.0210
3
GPF-plus
0.9583 ±0.0419
34
MLP
0.9230 ±0.0070
53
GraphSAGE
0.9000 ±0.0365
100
GPF
actual #100 vs paper #615 515 places worse
0.8740 ±0.0340
best reported
actual #100 vs paper #615 515 places worse
paper 0.3483 ±0.1664
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)
paper 0.3483 ±0.1664 Δ at pub 0.5257
582
UniPrompt
0.4983 ±0.1785
This paper
609
Linear-probe
0.3832 ±0.1361
This paper
612
Fine-tune
0.3750 ±0.1357
This paper
614
GPPT
0.3516 ±0.1512
This paper
615
EdgePrompt+
0.3502 ±0.1661
This paper
617
All-In-One
actual #617 vs paper #617
0.3153 ±0.1314
actual #617 vs paper #617
paper 0.3153 ±0.1314

Improvement within reported uncertainty; not highlighted.

paper 0.3153 ±0.1314 Δ at pub 0.1661
618
GraphPrompt
0.3019 ±0.1363
This paper
#ModelAccuracy ↑Paper
1
P^2GNN
0.9541 ±0.0272
2
ACM-GCN
0.9480 ±0.0380
3
RF-GCN
0.9429
24
MLP
0.9136 ±0.0070
138
SAGE
0.8269
459
UniPrompt
0.5280 ±0.1108
This paper
560
GPF
actual #560 vs paper #571 11 places worse
0.3622 ±0.0946
best reported
actual #560 vs paper #571 11 places worse
paper 0.2891 ±0.0885

Difference within reported uncertainty; not counted as underperformance.

paper 0.2891 ±0.0885 Δ today 0.0731
562
Fine-tune
0.3582 ±0.1130
This paper
563
GPPT
actual #563 vs paper #571 8 places worse
0.2901 ±0.0832
actual #563 vs paper #571 8 places worse
paper 0.2901 ±0.0832
564
Linear-probe
0.3492 ±0.0974
This paper
567
GraphPrompt
actual #567 vs paper #576 9 places worse
0.3243 ±0.1081
best reported
actual #567 vs paper #576 9 places worse
paper 0.2382 ±0.0750

Difference within reported uncertainty; not counted as underperformance.

paper 0.2382 ±0.0750 Δ today 0.0861
568
EdgePrompt+
0.3213 ±0.0742
This paper
573
All-In-One
actual #573 vs paper #573
0.2667 ±0.1242
actual #573 vs paper #573
paper 0.2667 ±0.1242

Improvement within reported uncertainty; not highlighted.

paper 0.2667 ±0.1242 Δ at pub 0.1326
#ModelAccuracy ↑Paper
1
DiGGR
0.4535 ±0.0353
2
TRIGON
0.4402 ±0.0028
3
DoG
0.4320 ±0.0120
42
MLP
0.4026 ±0.0108
68
GraphSAGE
0.3899 ±0.0085
382
GPF
actual #382 vs paper #481 99 places worse
0.2870 ±0.0335
best reported
actual #382 vs paper #481 99 places worse
paper 0.2081 ±0.0308
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)
paper 0.2081 ±0.0308 Δ at pub 0.0789
419
UniPrompt
0.2623 ±0.0446
This paper
440
All-In-One
actual #440 vs paper #480 40 places worse
0.2461 ±0.0280
best reported
actual #440 vs paper #480 40 places worse
paper 0.2108 ±0.0217
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)

Difference within reported uncertainty; not counted as underperformance.

paper 0.2108 ±0.0217 Δ at pub 0.0353
462
GPPT
actual #462 vs paper #488 26 places worse
0.2258 ±0.0197
best reported
actual #462 vs paper #488 26 places worse
paper 0.1981 ±0.0163
best at pub: ProG: A Graph Prompt Learning Benchmark (NeurIPS 2024)

Difference within reported uncertainty; not counted as underperformance.

paper 0.1981 ±0.0163 Δ at pub 0.0277
478
Fine-tune
0.2136 ±0.0328
This paper
479
EdgePrompt+
0.2136 ±0.0276
This paper
480
Linear-probe
0.2133 ±0.0262
This paper
488
GraphPrompt
0.1984 ±0.0279
This paper
#ModelAccuracy ↑Paper
1
Hetero-S (GAT 8-layer)
0.8693
2
Dir-GNN+CNA
0.8586 ±0.0180
3
GAT
0.8560
52
GCN
0.7033
169
MLP
0.5429
276
GraphPrompt
actual #276 vs paper #276
0.2828 ±0.0438
actual #276 vs paper #276
paper 0.2828 ±0.0438

Improvement within reported uncertainty; not highlighted.

paper 0.2828 ±0.0438 Δ at pub 0.0292
280
UniPrompt
0.2667 ±0.0251
This paper
281
Fine-tune
0.2622 ±0.0273
This paper
282
GPF
actual #282 vs paper #282
0.2612 ±0.0375
best reported
actual #282 vs paper #282
paper 0.2603 ±0.0437

Difference within reported uncertainty; not counted as underperformance.

paper 0.2603 ±0.0437 Δ at pub 0.0009
284
GPPT
0.2546 ±0.0543
This paper
285
Linear-probe
0.2427 ±0.0384
This paper
286
EdgePrompt+
0.2379 ±0.0331
This paper
288
All-In-One
0.2241 ±0.0358
This paper
#ModelAccuracy ↑Paper
1
IBG-NN
0.7763 ±0.0179
2
Dir-GNN+CNA
0.7747 ±0.0128
3
DHGNN
0.7684 ±0.0161
46
GCN
0.6067
172
MLP
0.3930 ±0.0079
267
UniPrompt
0.2420 ±0.0235
This paper
270
GraphPrompt
0.2285 ±0.0328
This paper
272
Linear-probe
0.2282 ±0.0410
This paper
275
Fine-tune
0.2227 ±0.0410
This paper
277
All-In-One
0.2203 ±0.0246
This paper
278
EdgePrompt+
0.2199 ±0.0250
This paper
279
GPF
0.2166 ±0.0328
This paper
280
GPPT
0.2156 ±0.0230
This paper
SOTA performance (not significantly different from the best) Proposed method (this paper) Baseline / comparison (this paper) Global context (other papers) Best at pub — reported result worse than the best known when published (best reported in green) Best at pub — reported value improved over the best known when published Best today — OK at publication; today's leaderboard best is elsewhere